dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Varibaculum cambriense

Lineage

Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Actinomycetaceae; Varibaculum; Varibaculum cambriense

CAZyme ID

MGYG000002897_00502

CAZy Family

CBM48

CAZyme Description

Glycogen operon protein GlgX

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
749		83039.8	4.9365

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002897	2017891	MAG	United States	North America

Gene Location

Start: 127014; End: 129263 Strand: -

Enzyme Prediction help

EC	3.2.1.68	3.2.1.-	2.4.1.25

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH13	199	583	1.7e-140	0.9971509971509972
CBM48	26	118	9.6e-16	0.9078947368421053

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
TIGR02100	glgX_debranch	0.0	23	744	3	688	glycogen debranching enzyme GlgX. This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. In the wide band between the trusted and noise cutoffs are functionally similar enzymes, mostly from plants, that act similarly but usually are termed isoamylase. [Energy metabolism, Biosynthesis and degradation of polysaccharides]
cd11326	AmyAc_Glg_debranch	0.0	165	625	4	433	Alpha amylase catalytic domain found in glycogen debranching enzymes. Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities: 4-alpha-D-glucanotransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). 4-alpha-D-glucanotransferase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. In Escherichia coli, GlgX is the debranching enzyme and malQ is the 4-alpha-glucanotransferase. TreX, an archaeal glycogen-debranching enzyme has dual activities like mammals and yeast, but is structurally similar to GlgX. TreX exists in two oligomeric states, a dimer and tetramer. Isoamylase (EC 3.2.1.68) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen and their beta-limit dextrins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
PRK03705	PRK03705	0.0	24	702	9	625	glycogen debranching protein GlgX.
COG1523	PulA	0.0	6	716	1	672	Pullulanase/glycogen debranching enzyme [Carbohydrate transport and metabolism].
PRK14510	PRK14510	1.54e-173	24	678	13	622	bifunctional glycogen debranching protein GlgX/4-alpha-glucanotransferase.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QOX82273.1	0.0	12	744	12	745
QDC26724.1	3.56e-289	24	743	13	733
QQC44274.1	8.93e-284	24	747	22	757
AKU65045.1	3.36e-281	24	747	22	757
QGS11211.1	1.45e-277	24	745	22	755

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2VNC_A	7.79e-173	9	724	4	692	Crystalstructure of Glycogen Debranching enzyme TreX from Sulfolobus solfataricus [Saccharolobus solfataricus],2VNC_B Crystal structure of Glycogen Debranching enzyme TreX from Sulfolobus solfataricus [Saccharolobus solfataricus],2VR5_A Crystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose intermediate and glucose [Saccharolobus solfataricus],2VR5_B Crystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose intermediate and glucose [Saccharolobus solfataricus],2VUY_A Crystal structure of Glycogen Debranching exzyme TreX from Sulfolobus solfatarius [Saccharolobus solfataricus],2VUY_B Crystal structure of Glycogen Debranching exzyme TreX from Sulfolobus solfatarius [Saccharolobus solfataricus],7EAV_A Chain A, Glycogen debranching enzyme [Saccharolobus solfataricus],7EAV_B Chain B, Glycogen debranching enzyme [Saccharolobus solfataricus]
2WSK_A	7.63e-153	24	702	9	625	Crystalstructure of Glycogen Debranching Enzyme GlgX from Escherichia coli K-12 [Escherichia coli K-12]
4J7R_A	1.88e-100	21	745	59	813	CrystalStructure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1) [Chlamydomonas reinhardtii],4J7R_B Crystal Structure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1) [Chlamydomonas reinhardtii],4OKD_A Crystal Structure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1) in complex with maltoheptaose [Chlamydomonas reinhardtii],4OKD_B Crystal Structure of Chlamydomonas reinhardtii Isoamylase 1 (ISA1) in complex with maltoheptaose [Chlamydomonas reinhardtii]
1BF2_A	9.42e-91	32	713	14	711	StructureOf Pseudomonas Isoamylase [Pseudomonas amyloderamosa]
2WAN_A	7.67e-40	27	629	318	831	Pullulanasefrom Bacillus acidopullulyticus [Bacillus acidopullulyticus]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P0A4Y5	4.65e-169	12	662	14	628	Glycogen operon protein GlgX homolog OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) OX=233413 GN=glgX PE=3 SV=1
P9WQ24	4.65e-169	12	662	14	628	Glycogen operon protein GlgX homolog OS=Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) OX=83331 GN=glgX PE=3 SV=1
P9WQ25	4.65e-169	12	662	14	628	Glycogen operon protein GlgX homolog OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=glgX PE=1 SV=1
B2VJR7	1.13e-158	17	703	4	625	Glycogen debranching enzyme OS=Erwinia tasmaniensis (strain DSM 17950 / CFBP 7177 / CIP 109463 / NCPPB 4357 / Et1/99) OX=465817 GN=glgX PE=3 SV=1
A8AQY2	7.62e-156	20	702	7	625	Glycogen debranching enzyme OS=Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) OX=290338 GN=glgX PE=3 SV=1

SignalP and Lipop Annotations help

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000032	0.000001	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000002897_00502.

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